Maybe a cleaning job will help. The fan could be terribly dirty and not very helpful. Both of my two Laptops (P3 500/800MHZ) have gentoo on it and survived several Gentoo/BSD/Slackware installations. But I clean them every year, and it's always a lot of dirt that comes out.

How much memory you have? Maybe your system pages heavily _and_ is compiling. That could be too much. Maybe sitting in a fridge would be better

hmm I had the same problem with my toshiba laptop..
because acpi wouldnt run (my toshiba was blacklisted in the kernel, after talking to the acpi guy this shouldnt be there.. so a little comment in the source fixed that )
my fan didnt start runnig (so laptop didnt cool enough).

My solution (before fixing acpi) was to run the toshiba tools and turn on the fan manualy.